Introduction
FungiExpresZ is a web based platform to analyze and visualize fungal gene expression data. It allows you to analyze and visualize …
- NCBI SRA fungal gene expression data.
- User uploaded gene expression data.
- NCBI SRA data combined with User uploaded data (1+2).
It contains normalized gene expression values of more than 12,000 NCBI SRA data from 8 different fungal species and, gene annotations and GO data of more than 100 different fungal species. For 3 strategies mentioned above, you can generate 12 different data exploratory plots and 6 different GO plots.
Data exploratory plots
- Scatter plot
- Multi-scatter plot
- CorrHeatBox
- Density plot
- Histogram
- Joy plot
- Box plot
- Violin plot
- Bar plot
- PCA plot
- Line plot
- Heatmap
GO plots
- EMAP plot
- CNET plot
- Dot plot
- Bar plot
- Heat box
- Upset plot
The purpose of this document is to explain all the key functionalities and methods used in this website wherever necessary.
User manual
Source
There are three ways in which you can access FungiExpresZ.
- Online
FungiExpresZ has been hoisted on shinyapps.io and can be accessed through the link https://cparsania.shinyapps.io/FungiExpresZ/. This is one of the quickest way to access the FungiExpresZ. However, due to limited computational resources, I would recommend this approach only when the size of the data is comparatively small (< 10 MB) and/or you are in a need of quick figure out of your data. Current setup allows approx. 30 users to concurrently
As an R package
As a docker container
Home screen
FIGURE 1: FungiExpresZ home screen
Select/Upload data
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Select SRA data
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FIGURE 2: FungiExpresZ select SRA data
Upload user data
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FIGURE 3: FungiExpresZ upload user data
Assign groups
Sample groups
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FIGURE 4: FungiExpresZ define sample groups
Gene groups
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FIGURE 5: FungiExpresZ define gene groups
View active groups
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Plot panels
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Plot input panels
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Scatter plot
FIGURE XXX: FungiExpresZ Scatter plot input panel
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Multi-scatter plot, CorrHeatBox, Density plot, Histogram, Joy plot, Box plot, Violin plot and PCA plot
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FIGURE XXX: FungiExpresZ Multi-scatter plot, CorrHeatBox, Density plot, Histogram, Joy plot, Box plot. Violin plot and PCA plot input panel
Bar plot inputs
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FIGURE XXX:FungiExpresZ Bar plot input panel
Line plot inputs
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FIGURE XXX: FungiExpresZ Line plot input panel
Heatmap inputs
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FIGURE XXX: FungiExpresZ Heatmap inputs
Plot settings
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FIGURE XXX: FungiExpresZ common plot settings : Theme and Legend (left), Labels & Title (right)
Plot specific settings
Scatter plot
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FIGURE XXX: FungiExpresZ Scatter plot advance options
Multi-scatter plot
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FIGURE XXX: FungiExpresZ Multi-scatter plot advance options
CorrHeatBox
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FIGURE XXX: FungiExpresZ Corr heat-box advance options
Density plot
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FIGURE XXX: FungiExpresZ Density plot advance options
Histogram
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FIGURE XXX: FungiExpresZ Histogram advance options
Joy plot
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FIGURE XXX: FungiExpresZ Joy plot advance options
Box plot
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FIGURE XXX: FungiExpresZ Box plot advance options
Violin plot
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FIGURE XXX: FungiExpresZ Violin plot advance options
Bar plot
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FIGURE XXX: FungiExpresZ Bar plot advance options
PCA plot
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FIGURE XXX: FungiExpresZ PCA plot advance options
Line plot
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FIGURE XXX: FungiExpresZ Line plot advance options
Heatmap
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GO analysis and visualizations
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FIGURE XXX: FungiExpresZ GO analysis inputs
GO plots specific settings
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Dot plot and Bar plot
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FIGURE XXX: FungiExpresZ GO Dot plot and Bar plot advance options
EMAP plot
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FIGURE XXX: FungiExpresZ GO EMAP plot advance options
CNET plot
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FIGURE XXX: FungiExpresZ GO CNET plot advance options
UPSET plot
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FIGURE XXX: FungiExpresZ GO Upset plot advance options
Heat plot
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FIGURE XXX: FungiExpresZ GO Heat plot advance options
Other panels
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About
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FIGURE XXX: FungiExpresZ Overview page
FIGURE XXX: FungiExpresZ Tutorial page
Downloads
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FIGURE XXX: FungiExpresZ Downloads --> Gene expression data page
FIGURE XXX: FungiExpresZ Download --> GO data page
News & Updates
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FIGURE XXX: FungiExpresZ News & Updates page
Citations
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FIGURE XXX: FungiExpresZ Citations page